CVE-2026-31969

{"dataType": "CVE_RECORD", "dataVersion": "5.2", "cveMetadata": {"cveId": "CVE-2026-31969", "assignerOrgId": "a0819718-46f1-4df5-94e2-005712e83aaa", "state": "PUBLISHED", "assignerShortName": "GitHub_M", "dateReserved": "2026-03-10T15:40:10.485Z", "datePublished": "2026-03-18T19:47:44.893Z", "dateUpdated": "2026-03-18T20:12:53.495Z"}, "containers": {"cna": {"title": "HTSlib CRAM decoder has a heap buffer overflow", "problemTypes": [{"descriptions": [{"cweId": "CWE-122", "lang": "en", "description": "CWE-122: Heap-based Buffer Overflow", "type": "CWE"}]}, {"descriptions": [{"cweId": "CWE-787", "lang": "en", "description": "CWE-787: Out-of-bounds Write", "type": "CWE"}]}], "metrics": [{"cvssV4_0": {"attackVector": "NETWORK", "attackComplexity": "LOW", "attackRequirements": "NONE", "privilegesRequired": "NONE", "userInteraction": "PASSIVE", "vulnConfidentialityImpact": "NONE", "vulnIntegrityImpact": "HIGH", "vulnAvailabilityImpact": "LOW", "subConfidentialityImpact": "NONE", "subIntegrityImpact": "NONE", "subAvailabilityImpact": "NONE", "baseScore": 7.1, "baseSeverity": "HIGH", "vectorString": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N", "version": "4.0"}}], "references": [{"name": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc", "tags": ["x_refsource_CONFIRM"], "url": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc"}, {"name": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4", "tags": ["x_refsource_MISC"], "url": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4"}], "affected": [{"vendor": "samtools", "product": "htslib", "versions": [{"version": "< 1.21.1", "status": "affected"}, {"version": ">= 1.22, < 1.22.2", "status": "affected"}, {"version": "= 1.23", "status": "affected"}]}], "providerMetadata": {"orgId": "a0819718-46f1-4df5-94e2-005712e83aaa", "shortName": "GitHub_M", "dateUpdated": "2026-03-18T19:47:44.893Z"}, "descriptions": [{"lang": "en", "value": "HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue."}], "source": {"advisory": "GHSA-q4cj-f4h5-fqgc", "discovery": "UNKNOWN"}}, "adp": [{"metrics": [{"other": {"type": "ssvc", "content": {"timestamp": "2026-03-18T20:12:27.506059Z", "id": "CVE-2026-31969", "options": [{"Exploitation": "none"}, {"Automatable": "no"}, {"Technical Impact": "partial"}], "role": "CISA Coordinator", "version": "2.0.3"}}}], "title": "CISA ADP Vulnrichment", "providerMetadata": {"orgId": "134c704f-9b21-4f2e-91b3-4a467353bcc0", "shortName": "CISA-ADP", "dateUpdated": "2026-03-18T20:12:53.495Z"}}]}}

{"dataType": "CVE_RECORD", "containers": {"adp": [{"title": "CISA ADP Vulnrichment", "metrics": [{"other": {"type": "ssvc", "content": {"id": "CVE-2026-31969", "role": "CISA Coordinator", "options": [{"Exploitation": "none"}, {"Automatable": "no"}, {"Technical Impact": "partial"}], "version": "2.0.3", "timestamp": "2026-03-18T20:12:27.506059Z"}}}], "providerMetadata": {"orgId": "134c704f-9b21-4f2e-91b3-4a467353bcc0", "shortName": "CISA-ADP", "dateUpdated": "2026-03-18T20:12:46.162Z"}}], "cna": {"title": "HTSlib CRAM decoder has a heap buffer overflow", "source": {"advisory": "GHSA-q4cj-f4h5-fqgc", "discovery": "UNKNOWN"}, "metrics": [{"cvssV4_0": {"version": "4.0", "baseScore": 7.1, "attackVector": "NETWORK", "baseSeverity": "HIGH", "vectorString": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N", "userInteraction": "PASSIVE", "attackComplexity": "LOW", "attackRequirements": "NONE", "privilegesRequired": "NONE", "subIntegrityImpact": "NONE", "vulnIntegrityImpact": "HIGH", "subAvailabilityImpact": "NONE", "vulnAvailabilityImpact": "LOW", "subConfidentialityImpact": "NONE", "vulnConfidentialityImpact": "NONE"}}], "affected": [{"vendor": "samtools", "product": "htslib", "versions": [{"status": "affected", "version": "< 1.21.1"}, {"status": "affected", "version": ">= 1.22, < 1.22.2"}, {"status": "affected", "version": "= 1.23"}]}], "references": [{"url": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc", "name": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc", "tags": ["x_refsource_CONFIRM"]}, {"url": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4", "name": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4", "tags": ["x_refsource_MISC"]}], "descriptions": [{"lang": "en", "value": "HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue."}], "problemTypes": [{"descriptions": [{"lang": "en", "type": "CWE", "cweId": "CWE-122", "description": "CWE-122: Heap-based Buffer Overflow"}]}, {"descriptions": [{"lang": "en", "type": "CWE", "cweId": "CWE-787", "description": "CWE-787: Out-of-bounds Write"}]}], "providerMetadata": {"orgId": "a0819718-46f1-4df5-94e2-005712e83aaa", "shortName": "GitHub_M", "dateUpdated": "2026-03-18T19:47:44.893Z"}}}, "cveMetadata": {"cveId": "CVE-2026-31969", "state": "PUBLISHED", "dateUpdated": "2026-03-18T20:12:53.495Z", "dateReserved": "2026-03-10T15:40:10.485Z", "assignerOrgId": "a0819718-46f1-4df5-94e2-005712e83aaa", "datePublished": "2026-03-18T19:47:44.893Z", "assignerShortName": "GitHub_M"}, "dataVersion": "5.2"}

{"affected": [{"affectedData": [{"product": "htslib", "vendor": "samtools", "versions": [{"status": "affected", "version": "< 1.21.1"}, {"status": "affected", "version": ">= 1.22, < 1.22.2"}, {"status": "affected", "version": "= 1.23"}]}], "source": "security-advisories@github.com"}], "configurations": [{"nodes": [{"cpeMatch": [{"criteria": "cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*", "matchCriteriaId": "A069D6B6-FFF6-4DB7-9811-A568ECC4B288", "versionEndExcluding": "1.21.1", "vulnerable": true}, {"criteria": "cpe:2.3:a:htslib:htslib:*:*:*:*:*:*:*:*", "matchCriteriaId": "D9D525C8-C8AD-4368-A396-EB4D9DA02B1C", "versionEndExcluding": "1.22.2", "versionStartIncluding": "1.22", "vulnerable": true}, {"criteria": "cpe:2.3:a:htslib:htslib:1.23:*:*:*:*:*:*:*", "matchCriteriaId": "AAA6BBB2-76F3-4372-9BAE-FDE157401EFD", "vulnerable": true}], "negate": false, "operator": "OR"}]}], "cveTags": [], "descriptions": [{"lang": "en", "value": "HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue."}, {"lang": "es", "value": "HTSlib es una biblioteca para leer y escribir formatos de archivo bioinform\u00e1ticos. CRAM es un formato comprimido que almacena datos de alineaci\u00f3n de secuencias de ADN utilizando una variedad de codificaciones y m\u00e9todos de compresi\u00f3n. Al leer datos codificados usando el m\u00e9todo 'BYTE_ARRAY_STOP', un error de uno de m\u00e1s en la comprobaci\u00f3n de la funci\u00f3n 'cram_byte_array_stop_decode_char()' para un b\u00fafer de salida lleno podr\u00eda resultar en que un solo byte controlado por el atacante se escriba m\u00e1s all\u00e1 del final de una asignaci\u00f3n de memoria din\u00e1mica. Explotar este error causa un desbordamiento de b\u00fafer de heap. Si un usuario abre un archivo dise\u00f1ado para explotar este problema, podr\u00eda llevar a que el programa falle, o a la sobrescritura de datos y estructuras de heap de maneras no esperadas por el programa. Podr\u00eda ser posible usar esto para obtener ejecuci\u00f3n de c\u00f3digo arbitrario. Las versiones 1.23.1, 1.22.2 y 1.21.1 incluyen correcciones para este problema. No hay soluci\u00f3n alternativa para este problema."}], "id": "CVE-2026-31969", "lastModified": "2026-06-17T10:34:51.773", "metrics": {"cvssMetricV31": [{"cvssData": {"attackComplexity": "LOW", "attackVector": "NETWORK", "availabilityImpact": "HIGH", "baseScore": 8.1, "baseSeverity": "HIGH", "confidentialityImpact": "NONE", "integrityImpact": "HIGH", "privilegesRequired": "NONE", "scope": "UNCHANGED", "userInteraction": "REQUIRED", "vectorString": "CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H", "version": "3.1"}, "exploitabilityScore": 2.8, "impactScore": 5.2, "source": "nvd@nist.gov", "type": "Primary"}], "cvssMetricV40": [{"cvssData": {"Automatable": "NOT_DEFINED", "Recovery": "NOT_DEFINED", "Safety": "NOT_DEFINED", "attackComplexity": "LOW", "attackRequirements": "NONE", "attackVector": "NETWORK", "availabilityRequirement": "NOT_DEFINED", "baseScore": 7.1, "baseSeverity": "HIGH", "confidentialityRequirement": "NOT_DEFINED", "exploitMaturity": "NOT_DEFINED", "integrityRequirement": "NOT_DEFINED", "modifiedAttackComplexity": "NOT_DEFINED", "modifiedAttackRequirements": "NOT_DEFINED", "modifiedAttackVector": "NOT_DEFINED", "modifiedPrivilegesRequired": "NOT_DEFINED", "modifiedSubAvailabilityImpact": "NOT_DEFINED", "modifiedSubConfidentialityImpact": "NOT_DEFINED", "modifiedSubIntegrityImpact": "NOT_DEFINED", "modifiedUserInteraction": "NOT_DEFINED", "modifiedVulnAvailabilityImpact": "NOT_DEFINED", "modifiedVulnConfidentialityImpact": "NOT_DEFINED", "modifiedVulnIntegrityImpact": "NOT_DEFINED", "privilegesRequired": "NONE", "providerUrgency": "NOT_DEFINED", "subAvailabilityImpact": "NONE", "subConfidentialityImpact": "NONE", "subIntegrityImpact": "NONE", "userInteraction": "PASSIVE", "valueDensity": "NOT_DEFINED", "vectorString": "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X", "version": "4.0", "vulnAvailabilityImpact": "LOW", "vulnConfidentialityImpact": "NONE", "vulnIntegrityImpact": "HIGH", "vulnerabilityResponseEffort": "NOT_DEFINED"}, "source": "security-advisories@github.com", "type": "Secondary"}], "ssvcV203": [{"source": "134c704f-9b21-4f2e-91b3-4a467353bcc0", "ssvcData": {"id": "CVE-2026-31969", "options": [{"exploitation": "none"}, {"automatable": "no"}, {"technicalImpact": "partial"}], "role": "CISA Coordinator", "timestamp": "2026-03-18T20:12:27.506059Z", "version": "2.0.3"}}]}, "published": "2026-03-18T20:16:21.743", "references": [{"source": "security-advisories@github.com", "tags": ["Patch"], "url": "https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4"}, {"source": "security-advisories@github.com", "tags": ["Patch", "Vendor Advisory"], "url": "https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc"}], "sourceIdentifier": "security-advisories@github.com", "vulnStatus": "Analyzed", "weaknesses": [{"description": [{"lang": "en", "value": "CWE-122"}, {"lang": "en", "value": "CWE-787"}], "source": "security-advisories@github.com", "type": "Secondary"}]}

{}

{"affected": [{"configurations": [{"platform": null, "status": "affected", "versions": {"scheme": "semver", "value": "[0,1.21.1)"}}, {"platform": null, "status": "affected", "versions": {"scheme": "semver", "value": "[1.22,1.22.2)"}}, {"platform": null, "status": "affected", "versions": {"scheme": "semver", "value": "1.23"}}], "enrichment": {"confidence": 100.0, "confidence_source": "cna", "scores": [{"score": 100.0, "source": "cna"}]}, "product": "htslib", "vendor": "samtools"}], "analysis": {"en": {"generated_at": "2026-03-19T15:57:15.314490+00:00", "value": {"mitigation_remediation": ["Apply the latest version of HTSLib (1.23.1 or newer) which includes the buffer overflow fix.", "Verify that your installation is not using a vulnerable version by checking the library version string.", "Until the library can be updated, avoid opening untrusted CRAM files or restrict file access to trusted users."], "summary": {"action": "Patch Immediately", "impact": "Remote Code Execution"}, "threat_synthesis": {"affected_systems": "The affected product is HTSLib, used by the Samtools toolkit. Versions 1.23.1, 1.22.2 and 1.21.1 contain the fix, meaning any installation of earlier releases\u2014including 1.23.0 and prior\u2014is vulnerable. The issue is specific to the CRAM decoding component of the library.", "description_and_impact": "An out-by-one error in HTSlib's cram_byte_array_stop_decode_char() function allows the CRAM decoder to write a single byte past the end of a dynamically allocated buffer when processing data encoded with the BYTE_ARRAY_STOP method. This heap buffer overflow can cause the application to crash or corrupt memory and may, in certain circumstances, enable an attacker to execute arbitrary code. The vulnerability is classified as CWE-122 and CWE-787.", "risk_and_exploitability": "The CVSS score is 7.1, indicating a high severity. The EPSS score is below 1%, suggesting low exploitation probability in the wild, and the vulnerability is not listed in CISA's KEV catalog. Attackers would need to supply a malicious CRAM file that uses the BYTE_ARRAY_STOP encoding to trigger the overflow, which typically requires local access or the ability to influence the data the program reads."}}}}, "created": "2026-03-19T08:55:38.552562+00:00", "updated": "2026-03-25T11:52:20.712183+00:00", "vendors": ["samtools", "samtools$PRODUCT$htslib"]}